Revision 9949
Added by Aaron Marcuse-Kubitza over 11 years ago
| inputs/IRMNG/genus_homonyms/test.xml.ref | ||
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Put template: |
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<VegBIEN> |
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<_setDefault id="-1"> |
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<source_id><source><shortname>IRMNG</shortname></source></source_id> |
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<path> |
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<_simplifyPath> |
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<next>parent_id</next> |
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<path> |
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<location> |
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<locationevent> |
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<taxonoccurrence> |
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<taxondetermination> |
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<taxonverbatim_id> |
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<taxonverbatim> |
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<taxonlabel_id> |
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<taxonlabel> |
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<parent_id> |
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<taxonlabel> |
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<rank>$taxonRank</rank> |
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<parent_id> |
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<taxonlabel> |
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<rank>cultivar</rank> |
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<parent_id> |
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<taxonlabel> |
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<rank>forma</rank> |
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<parent_id> |
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<taxonlabel> |
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<rank>variety</rank> |
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<parent_id> |
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<taxonlabel> |
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<rank>subspecies</rank> |
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<parent_id> |
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<taxonlabel> |
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<rank>species</rank> |
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<taxonepithet>$specificEpithet</taxonepithet> |
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<parent_id> |
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<taxonlabel> |
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<rank>genus</rank> |
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<taxonepithet>$genus</taxonepithet> |
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<parent_id> |
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<taxonlabel> |
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<rank>family</rank> |
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<taxonepithet>$family</taxonepithet> |
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<parent_id> |
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<taxonlabel> |
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<rank>order</rank> |
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<taxonepithet>$order</taxonepithet> |
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<parent_id> |
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<taxonlabel> |
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<rank>class</rank> |
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<taxonepithet>$class</taxonepithet> |
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<parent_id> |
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<taxonlabel> |
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<rank>phylum</rank> |
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<taxonepithet>$phylum</taxonepithet> |
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<parent_id> |
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<taxonlabel> |
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<rank>kingdom</rank> |
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<taxonepithet>$kingdom</taxonepithet> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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<rank>$taxonRank</rank> |
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<sourceaccessioncode>$taxonID</sourceaccessioncode> |
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<taxonepithet> |
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<_if name="if taxonomic name is epithet"> |
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<cond> |
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<_alt> |
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<2>true</2> |
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<1><_taxonomic_name_is_epithet><rank>$taxonRank</rank></_taxonomic_name_is_epithet></1> |
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</_alt> |
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</cond> |
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<then>$taxonNameOrEpithet</then> |
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</_if> |
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</taxonepithet> |
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<taxonomicname> |
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<_merge_prefix> |
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<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
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<value> |
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<_alt> |
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<2> |
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<_join_words> |
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<2><_filter_genus><value>$genus</value></_filter_genus></2> |
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<3>$specificEpithet</3> |
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</_join_words> |
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</2> |
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<3>$taxonNameOrEpithet</3> |
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</_alt> |
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</value> |
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</_merge_prefix> |
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</taxonomicname> |
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</taxonlabel> |
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</taxonlabel_id> |
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<family>$family</family> |
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<genus>$genus</genus> |
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<specific_epithet>$specificEpithet</specific_epithet> |
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<verbatimrank>$taxonRank</verbatimrank> |
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</taxonverbatim> |
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</taxonverbatim_id> |
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</taxondetermination> |
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</taxonoccurrence> |
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</locationevent> |
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</location> |
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</path> |
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</_simplifyPath> |
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</path> |
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</_setDefault> |
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</VegBIEN> |
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Inserted 19 new rows into database |
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| inputs/IRMNG/genus_homonyms/new_terms.csv | ||
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| 1 |
IRMNG_ID,taxonID,, |
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Homonym,taxonNameOrEpithet,, |
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Homonym_Rank,taxonRank,, |
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Authority,authors,, |
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| inputs/IRMNG/homonyms.run | ||
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#!/bin/bash -e |
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. "$(dirname "${BASH_SOURCE[0]}")"/table.run
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. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/sh/web.sh
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if self_not_included; then |
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*.htm/make() |
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{
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echo_func; set_make_vars; check_wildcard_target_exists |
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local letter_range="${letter_range-[A-Z]}"
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local rank="${table%_homonyms}"
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curl --output '#1.htm' "http://www.marine.csiro.au/mirrorsearch/ir_search.list_homonyms?hlevel=$rank&start_letter=$letter_range&restrict_by=pln&output_style=delim_rows" |
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} |
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*.txt/make() |
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{
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echo_func; set_make_vars; deferred_check_target_exists |
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*.htm/make |
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for in in "$top_dir"/*.htm; do |
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stdout="${in/%.htm/.txt}" to_file grep -vE '^<' "$in" # strip tags
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done |
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} |
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func_override import__table_run |
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import() |
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{
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echo_func; set_make_vars |
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*.txt/make |
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self_make import__table_run "$@" |
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} |
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|
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fi |
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| 0 | 33 | |
| inputs/IRMNG/Source/map.csv | ||
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IRMNG,VegCore,Filter,Comments |
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:primary database,sourceType,, |
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| inputs/IRMNG/Source/VegBIEN.csv | ||
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| 1 |
IRMNG,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
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:primary database,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
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| inputs/IRMNG/Source/test.xml.ref | ||
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| 1 |
Put template: |
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<VegBIEN> |
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<_setDefault id="-1"> |
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<source_id><source><shortname>IRMNG</shortname></source></source_id> |
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<path> |
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<_simplifyPath> |
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<next>parent_id</next> |
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<path> |
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<source> |
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<shortname>IRMNG</shortname> |
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<sourcetype>primary database</sourcetype> |
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</source> |
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</path> |
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</_simplifyPath> |
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</path> |
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</_setDefault> |
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</VegBIEN> |
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Inserted 0 new rows into database |
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| inputs/IRMNG/species_homonyms/header.csv | ||
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| 1 |
*row_num,taxonID,taxonNameOrEpithet,taxonRank,authors,kingdom,phylum,class,order,family,genus,specificEpithet |
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| inputs/IRMNG/species_homonyms/run | ||
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| 1 |
#!/bin/bash -e |
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. "$(dirname "${BASH_SOURCE[0]}")"/../homonyms.run
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letter_range={A} # [A] does not work
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| inputs/IRMNG/species_homonyms/map.csv | ||
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IRMNG,VegCore,Filter,Comments |
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*row_num,*row_num,, |
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taxonID,taxonID,, |
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taxonNameOrEpithet,taxonNameOrEpithet,, |
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taxonRank,taxonRank,, |
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authors,authors,, |
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kingdom,kingdom,, |
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phylum,phylum,, |
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class,class,, |
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order,order,, |
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family,family,, |
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genus,genus,, |
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specificEpithet,specificEpithet,, |
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| inputs/IRMNG/species_homonyms/test.xml.ref | ||
|---|---|---|
| 1 |
Put template: |
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| 2 |
<VegBIEN> |
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<_setDefault id="-1"> |
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<source_id><source><shortname>IRMNG</shortname></source></source_id> |
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<path> |
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<_simplifyPath> |
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<next>parent_id</next> |
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<path> |
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<location> |
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<locationevent> |
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<taxonoccurrence> |
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<taxondetermination> |
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<taxonverbatim_id> |
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<taxonverbatim> |
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<taxonlabel_id> |
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<taxonlabel> |
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<parent_id> |
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<taxonlabel> |
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<rank>$taxonRank</rank> |
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<parent_id> |
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<taxonlabel> |
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<rank>cultivar</rank> |
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| 23 |
<parent_id> |
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| 24 |
<taxonlabel> |
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<rank>forma</rank> |
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| 26 |
<parent_id> |
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| 27 |
<taxonlabel> |
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<rank>variety</rank> |
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| 29 |
<parent_id> |
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| 30 |
<taxonlabel> |
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<rank>subspecies</rank> |
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<parent_id> |
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<taxonlabel> |
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<rank>species</rank> |
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<taxonepithet>$specificEpithet</taxonepithet> |
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<parent_id> |
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<taxonlabel> |
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<rank>genus</rank> |
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<taxonepithet>$genus</taxonepithet> |
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<parent_id> |
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<taxonlabel> |
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<rank>family</rank> |
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<taxonepithet>$family</taxonepithet> |
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<parent_id> |
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<taxonlabel> |
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<rank>order</rank> |
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<taxonepithet>$order</taxonepithet> |
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<parent_id> |
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<taxonlabel> |
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<rank>class</rank> |
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<taxonepithet>$class</taxonepithet> |
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<parent_id> |
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<taxonlabel> |
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<rank>phylum</rank> |
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<taxonepithet>$phylum</taxonepithet> |
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<parent_id> |
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<taxonlabel> |
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<rank>kingdom</rank> |
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<taxonepithet>$kingdom</taxonepithet> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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</taxonlabel> |
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</parent_id> |
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<rank>$taxonRank</rank> |
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<sourceaccessioncode>$taxonID</sourceaccessioncode> |
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<taxonepithet> |
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<_if name="if taxonomic name is epithet"> |
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<cond> |
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<_alt> |
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<2>true</2> |
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<1><_taxonomic_name_is_epithet><rank>$taxonRank</rank></_taxonomic_name_is_epithet></1> |
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</_alt> |
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</cond> |
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<then>$taxonNameOrEpithet</then> |
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</_if> |
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</taxonepithet> |
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<taxonomicname> |
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<_merge_prefix> |
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<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
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<value> |
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<_alt> |
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<2> |
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<_join_words> |
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<2><_filter_genus><value>$genus</value></_filter_genus></2> |
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<3>$specificEpithet</3> |
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</_join_words> |
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</2> |
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<3>$taxonNameOrEpithet</3> |
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</_alt> |
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</value> |
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</_merge_prefix> |
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| 112 |
</taxonomicname> |
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| 113 |
</taxonlabel> |
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</taxonlabel_id> |
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<family>$family</family> |
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| 116 |
<genus>$genus</genus> |
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<specific_epithet>$specificEpithet</specific_epithet> |
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<verbatimrank>$taxonRank</verbatimrank> |
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| 119 |
</taxonverbatim> |
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| 120 |
</taxonverbatim_id> |
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| 121 |
</taxondetermination> |
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| 122 |
</taxonoccurrence> |
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| 123 |
</locationevent> |
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| 124 |
</location> |
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| 125 |
</path> |
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| 126 |
</_simplifyPath> |
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</path> |
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| 128 |
</_setDefault> |
|
| 129 |
</VegBIEN> |
|
| 130 |
Inserted 19 new rows into database |
|
| inputs/IRMNG/species_homonyms/VegBIEN.csv | ||
|---|---|---|
| 1 |
IRMNG,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Filter; Comments,Comments |
|
| 2 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
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| 3 |
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet", |
|
| 4 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet", |
|
| 5 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet", |
|
| 6 |
order,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=order]/taxonepithet", |
|
| 7 |
class,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=class]/taxonepithet", |
|
| 8 |
phylum,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=phylum]/taxonepithet", |
|
| 9 |
kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,phylum,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=kingdom]/taxonepithet", |
|
| 10 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
|
| 11 |
taxonID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode, |
|
| 12 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank", |
|
| 13 |
taxonNameOrEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/then", |
|
| 14 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 15 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value, |
|
| 16 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1, |
|
| 17 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 18 |
taxonNameOrEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/3, |
|
| 19 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 20 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 21 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 22 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
|
| 23 |
*row_num,,** No join mapping for *row_num ** |
|
| 24 |
authors,,** No join mapping for authors ** |
|
| inputs/IRMNG/species_homonyms/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*row_num |
|
| 2 |
authors |
|
| inputs/IRMNG/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/import.run
|
|
| 3 |
|
|
| 4 |
if self_not_included; then |
|
| 5 |
|
|
| 6 |
subdirs=(family_homonyms genus_homonyms species_homonyms) |
|
| 7 |
|
|
| 8 |
import() |
|
| 9 |
{
|
|
| 10 |
echo_func |
|
| 11 |
fwd "$FUNCNAME" "$@" |
|
| 12 |
} |
|
| 13 |
|
|
| 14 |
fi |
|
| 0 | 15 | |
| inputs/IRMNG/map.csv | ||
|---|---|---|
| 1 |
IRMNG,VegCore,Filter,Comments |
|
| 2 |
row_num,*row_num,, |
|
| 3 |
IRMNG_ID,*taxonID,, |
|
| 4 |
Homonym,*taxonNameOrEpithet,, |
|
| 5 |
Homonym_Rank,*taxonRank,, |
|
| 6 |
Authority,*Author,, |
|
| 7 |
Kingdom,kingdom,, |
|
| 8 |
Phylum,phylum,, |
|
| 9 |
Class,class,, |
|
| 10 |
Order,order,, |
|
| 11 |
Family,family,, |
|
| 12 |
Genus,genus,, |
|
| 13 |
Species$,specificEpithet,,see species_homonyms for example values |
|
| inputs/IRMNG/family_homonyms/header.csv | ||
|---|---|---|
| 1 |
row_num,IRMNG_ID,Homonym,Homonym_Rank,Authority,Kingdom,Phylum,Class,Order,Family,Genus,Species$ |
|
| inputs/IRMNG/family_homonyms/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../homonyms.run
|
|
| 3 |
|
|
| 4 |
letter_range={A} # [A] does not work
|
|
| 0 | 5 | |
| inputs/IRMNG/family_homonyms/map.csv | ||
|---|---|---|
| 1 |
IRMNG,VegCore,Filter,Comments |
|
| 2 |
row_num,*row_num,, |
|
| 3 |
IRMNG_ID,taxonID,, |
|
| 4 |
Homonym,taxonNameOrEpithet,, |
|
| 5 |
Homonym_Rank,taxonRank,, |
|
| 6 |
Authority,authors,, |
|
| 7 |
Kingdom,kingdom,, |
|
| 8 |
Phylum,phylum,, |
|
| 9 |
Class,class,, |
|
| 10 |
Order,order,, |
|
| 11 |
Family,family,, |
|
| 12 |
Genus,genus,, |
|
| 13 |
Species$,specificEpithet,, |
|
| inputs/IRMNG/family_homonyms/test.xml.ref | ||
|---|---|---|
| 1 |
Put template: |
|
| 2 |
<VegBIEN> |
|
| 3 |
<_setDefault id="-1"> |
|
| 4 |
<source_id><source><shortname>IRMNG</shortname></source></source_id> |
|
| 5 |
<path> |
|
| 6 |
<_simplifyPath> |
|
| 7 |
<next>parent_id</next> |
|
| 8 |
<path> |
|
| 9 |
<location> |
|
| 10 |
<locationevent> |
|
| 11 |
<taxonoccurrence> |
|
| 12 |
<taxondetermination> |
|
| 13 |
<taxonverbatim_id> |
|
| 14 |
<taxonverbatim> |
|
| 15 |
<taxonlabel_id> |
|
| 16 |
<taxonlabel> |
|
| 17 |
<parent_id> |
|
| 18 |
<taxonlabel> |
|
| 19 |
<rank>$taxonRank</rank> |
|
| 20 |
<parent_id> |
|
| 21 |
<taxonlabel> |
|
| 22 |
<rank>cultivar</rank> |
|
| 23 |
<parent_id> |
|
| 24 |
<taxonlabel> |
|
| 25 |
<rank>forma</rank> |
|
| 26 |
<parent_id> |
|
| 27 |
<taxonlabel> |
|
| 28 |
<rank>variety</rank> |
|
| 29 |
<parent_id> |
|
| 30 |
<taxonlabel> |
|
| 31 |
<rank>subspecies</rank> |
|
| 32 |
<parent_id> |
|
| 33 |
<taxonlabel> |
|
| 34 |
<rank>species</rank> |
|
| 35 |
<taxonepithet>$specificEpithet</taxonepithet> |
|
| 36 |
<parent_id> |
|
| 37 |
<taxonlabel> |
|
| 38 |
<rank>genus</rank> |
|
| 39 |
<taxonepithet>$genus</taxonepithet> |
|
| 40 |
<parent_id> |
|
| 41 |
<taxonlabel> |
|
| 42 |
<rank>family</rank> |
|
| 43 |
<taxonepithet>$family</taxonepithet> |
|
| 44 |
<parent_id> |
|
| 45 |
<taxonlabel> |
|
| 46 |
<rank>order</rank> |
|
| 47 |
<taxonepithet>$order</taxonepithet> |
|
| 48 |
<parent_id> |
|
| 49 |
<taxonlabel> |
|
| 50 |
<rank>class</rank> |
|
| 51 |
<taxonepithet>$class</taxonepithet> |
|
| 52 |
<parent_id> |
|
| 53 |
<taxonlabel> |
|
| 54 |
<rank>phylum</rank> |
|
| 55 |
<taxonepithet>$phylum</taxonepithet> |
|
| 56 |
<parent_id> |
|
| 57 |
<taxonlabel> |
|
| 58 |
<rank>kingdom</rank> |
|
| 59 |
<taxonepithet>$kingdom</taxonepithet> |
|
| 60 |
</taxonlabel> |
|
| 61 |
</parent_id> |
|
| 62 |
</taxonlabel> |
|
| 63 |
</parent_id> |
|
| 64 |
</taxonlabel> |
|
| 65 |
</parent_id> |
|
| 66 |
</taxonlabel> |
|
| 67 |
</parent_id> |
|
| 68 |
</taxonlabel> |
|
| 69 |
</parent_id> |
|
| 70 |
</taxonlabel> |
|
| 71 |
</parent_id> |
|
| 72 |
</taxonlabel> |
|
| 73 |
</parent_id> |
|
| 74 |
</taxonlabel> |
|
| 75 |
</parent_id> |
|
| 76 |
</taxonlabel> |
|
| 77 |
</parent_id> |
|
| 78 |
</taxonlabel> |
|
| 79 |
</parent_id> |
|
| 80 |
</taxonlabel> |
|
| 81 |
</parent_id> |
|
| 82 |
</taxonlabel> |
|
| 83 |
</parent_id> |
|
| 84 |
<rank>$taxonRank</rank> |
|
| 85 |
<sourceaccessioncode>$taxonID</sourceaccessioncode> |
|
| 86 |
<taxonepithet> |
|
| 87 |
<_if name="if taxonomic name is epithet"> |
|
| 88 |
<cond> |
|
| 89 |
<_alt> |
|
| 90 |
<2>true</2> |
|
| 91 |
<1><_taxonomic_name_is_epithet><rank>$taxonRank</rank></_taxonomic_name_is_epithet></1> |
|
| 92 |
</_alt> |
|
| 93 |
</cond> |
|
| 94 |
<then>$taxonNameOrEpithet</then> |
|
| 95 |
</_if> |
|
| 96 |
</taxonepithet> |
|
| 97 |
<taxonomicname> |
|
| 98 |
<_merge_prefix> |
|
| 99 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
|
| 100 |
<value> |
|
| 101 |
<_alt> |
|
| 102 |
<2> |
|
| 103 |
<_join_words> |
|
| 104 |
<2><_filter_genus><value>$genus</value></_filter_genus></2> |
|
| 105 |
<3>$specificEpithet</3> |
|
| 106 |
</_join_words> |
|
| 107 |
</2> |
|
| 108 |
<3>$taxonNameOrEpithet</3> |
|
| 109 |
</_alt> |
|
| 110 |
</value> |
|
| 111 |
</_merge_prefix> |
|
| 112 |
</taxonomicname> |
|
| 113 |
</taxonlabel> |
|
| 114 |
</taxonlabel_id> |
|
| 115 |
<family>$family</family> |
|
| 116 |
<genus>$genus</genus> |
|
| 117 |
<specific_epithet>$specificEpithet</specific_epithet> |
|
| 118 |
<verbatimrank>$taxonRank</verbatimrank> |
|
| 119 |
</taxonverbatim> |
|
| 120 |
</taxonverbatim_id> |
|
| 121 |
</taxondetermination> |
|
| 122 |
</taxonoccurrence> |
|
| 123 |
</locationevent> |
|
| 124 |
</location> |
|
| 125 |
</path> |
|
| 126 |
</_simplifyPath> |
|
| 127 |
</path> |
|
| 128 |
</_setDefault> |
|
| 129 |
</VegBIEN> |
|
| 130 |
Inserted 14 new rows into database |
|
| inputs/IRMNG/family_homonyms/VegBIEN.csv | ||
|---|---|---|
| 1 |
IRMNG,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Filter; Comments,Comments |
|
| 2 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
|
| 3 |
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet", |
|
| 4 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet", |
|
| 5 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet", |
|
| 6 |
order,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=order]/taxonepithet", |
|
| 7 |
class,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=class]/taxonepithet", |
|
| 8 |
phylum,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=phylum]/taxonepithet", |
|
| 9 |
kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,phylum,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=kingdom]/taxonepithet", |
|
| 10 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
|
| 11 |
taxonID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode, |
|
| 12 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank", |
|
| 13 |
taxonNameOrEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/then", |
|
| 14 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 15 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value, |
|
| 16 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1, |
|
| 17 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 18 |
taxonNameOrEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/3, |
|
| 19 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 20 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 21 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 22 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
|
| 23 |
*row_num,,** No join mapping for *row_num ** |
|
| 24 |
authors,,** No join mapping for authors ** |
|
| inputs/IRMNG/family_homonyms/new_terms.csv | ||
|---|---|---|
| 1 |
IRMNG_ID,taxonID,, |
|
| 2 |
Homonym,taxonNameOrEpithet,, |
|
| 3 |
Homonym_Rank,taxonRank,, |
|
| 4 |
Authority,authors,, |
|
| inputs/IRMNG/family_homonyms/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*row_num |
|
| 2 |
authors |
|
| inputs/IRMNG/genus_homonyms/header.csv | ||
|---|---|---|
| 1 |
row_num,IRMNG_ID,Homonym,Homonym_Rank,Authority,Kingdom,Phylum,Class,Order,Family,Genus,Species$ |
|
| inputs/IRMNG/genus_homonyms/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../homonyms.run
|
|
| 0 | 3 | |
| inputs/IRMNG/genus_homonyms/map.csv | ||
|---|---|---|
| 1 |
IRMNG,VegCore,Filter,Comments |
|
| 2 |
row_num,*row_num,, |
|
| 3 |
IRMNG_ID,taxonID,, |
|
| 4 |
Homonym,taxonNameOrEpithet,, |
|
| 5 |
Homonym_Rank,taxonRank,, |
|
| 6 |
Authority,authors,, |
|
| 7 |
Kingdom,kingdom,, |
|
| 8 |
Phylum,phylum,, |
|
| 9 |
Class,class,, |
|
| 10 |
Order,order,, |
|
| 11 |
Family,family,, |
|
| 12 |
Genus,genus,, |
|
| 13 |
Species$,specificEpithet,, |
|
| inputs/IRMNG/genus_homonyms/VegBIEN.csv | ||
|---|---|---|
| 1 |
IRMNG,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Filter; Comments,Comments |
|
| 2 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
|
| 3 |
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet", |
|
| 4 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet", |
|
| 5 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet", |
|
| 6 |
order,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=order]/taxonepithet", |
|
| 7 |
class,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=class]/taxonepithet", |
|
| 8 |
phylum,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=phylum]/taxonepithet", |
|
| 9 |
kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,phylum,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=kingdom]/taxonepithet", |
|
| 10 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
|
| 11 |
taxonID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode, |
|
| 12 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank", |
|
| 13 |
taxonNameOrEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/then", |
|
| 14 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 15 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value, |
|
| 16 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1, |
|
| 17 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 18 |
taxonNameOrEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/3, |
|
| 19 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 20 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 21 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 22 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
|
| 23 |
*row_num,,** No join mapping for *row_num ** |
|
| 24 |
authors,,** No join mapping for authors ** |
|
| inputs/IRMNG/genus_homonyms/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*row_num |
|
| 2 |
authors |
|
| inputs/IRMNG/table.run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/table.run
|
|
| 0 | 3 | |
Also available in: Unified diff
added inputs/IRMNG/, including runscripts to download the names. this is now the 2nd datasource after GBIF to use runscripts, and the 3rd after FIA/GBIF to use new-style import.